Mitochondrial Genomic Characters Of Malacostracans And Sipunculans And The Molecular Evolutionary Research Based On Mitochondrial Genomes

Over the past decades, inference of a deeper phylogenetic relationship of metazoan with whole mitochondrial genome sequences has gained popularity. This resulted from many advantages offered over other molecular markers for phylogenetic analysis. Although more than one thousand and two hundreds mitochondrial genome sequences have been determined to date, the taxonomic sampling is still highly biased.Malacostracans have been the subject of a huge number of classificatory and phylogenetic studies employing morphological characters and molecular characters. Though Malacostraca itself is widely regarded as a monophyletic grouping, the relationships among the various groups of the Malacostraca are still controversial. In this paper, we report the mitochondrial genomes from the Litopenaeus vannamei Boone 1931, Fenneropenaeus chinensis Osbeck 1765, Exopalaemon carinicauda Holthuis 1950, Euphausia pacifica Hansen 1911 and Euphausia superba Dana 1852 (sampling from Prydz Bay, Antarctic). The mitochondrial genomes of them is 15, 989 bp, 16, 004 bp, 15, 730 bp, 16, 898 bp and more than 15, 498 bp in length (partial non-coding region was not determined), respectively.As seen in other metazoans, the genomes of L. vannamei, F. chinensis, Exopalaemon carinicauda and Euphausia pacifica contain a standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. However, the mitochondrial genome of Euphausia superba has an extra trnN gene compared with standard set of metazoan mitochondrial genomes. The gene arrangements of L. vannamei and F. chinensis mitochondrial genoms are consistent with the pancrustacean ground pattern. Unusual translocation of trnP and trnH was found when comparing with the pancrustacean ground pattern, which indicating gene order is not conserved among Caridea. Translocation of three tRNAs (trnL1, trnL2 and trnW) was found in the mitochondrial genome of Euphausia pacifica when comparing with the pancrustacean ground pattern. Besides the translocation of above three tRNAs, the duplication of trnN and translocation of trnI were founded in the mitochondrial genome of Euphausia superba. The largest non-coding region in the mitochondrial genome of Euphausia pacifica contains one section with tandem repeats (4.7×154 bp), which is the first report of largest tandem repeats (>150 bp) founded in the malacostracan mitochondrial genomes.All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea and Brachyura. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial PCGs strengthened the support that Caridea and Palinura are primitive members of Pleocyemata and that (((Penaeus+Fenneropenaeus)+Litopenaeus)+Marsupenaeus). The Euphausiacea clade was also recovered as monophyletic with strong statistical support. However, the taxonomic position and phylogenetic relationship of Euphausiacea within Malacostraca is unstable. The Bayesian analysis based on nucleotide and amino acid data strongly support the close relationship between Euphausiacea and Decapoda, which is coincidence with traditional views. The Neighbor-Joining approach based on nucleotide and amino acid data and Maximum-Likelihood analysis based on amino acid data strongly support the close relationship between Euphausiacea and Penaeidae, which destroy the monophyly of Decapoda and not coincidence with traditional classification. Nevertheless, the bootstrap value is very high, so the deeper analyses are needed.Sipunculans form a minor phylum of marine animals. Although the group was first documented in 1555, their taxonomic position within Metazoan is controversial. In this paper, we present here the sequence of Phascolosoma esculenta mitochondrial genome, the first one from phylum Sipuncula. The mitochondrial genome of the P. esculenta is 15, 494 bp in length and contains 13 PCGs, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. All of the 37 identified genes are transcribed from the same DNA strand. In comparison to typical metazoan mitochondrial genomes, sipunculid mitochondrial genome lacks trnR but has an extra trnM. From the analyses of mitochondrial genome of P. esculenta and other metazoan, we make the following conclusion: First, sipunculans and annelids (including echiurans) share similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; Second, phylogenetic analyses based on concatenated protein sequences also provide strong evidence that Sipuncula and Annelida (including echiurans) form a monophyletic clade to the exclusion of the Mollusca. Thus, many characteristics that have been hypothesized to link sipunculans with molluscs, including their developmental pattern and lack of segmentation, should be reevaluated.